rs2065706

Variant names:

• chr20-4702649-T-C
• rs2065706

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.174 in 152,024 control chromosomes in the GnomAD database, including 2,475 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26372 AN: 151906 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.191

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.174 AC: 26406 AN: 152024 Hom.: 2475 Cov.: 32 AF XY: 0.171 AC XY: 12712 AN XY: 74298

African (AFR) AF: 0.122 AC: 5068 AN: 41460

American (AMR) AF: 0.246 AC: 3758 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3472

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5160

South Asian (SAS) AF: 0.162 AC: 776 AN: 4800

European-Finnish (FIN) AF: 0.152 AC: 1611 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13648 AN: 67946

Other (OTH) AF: 0.190 AC: 401 AN: 2114

Alfa AF: 0.198 Hom.: 3711

Bravo AF: 0.179

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2065706; hg19: chr20-4683295;